After this mess my advice is download and use the combo installer and
avoid the Software Updater

I am quite sure, that you had a bad system before you tried the update.
My advise: Always check/repair the drive with apple´s drive tool or
disk warrior, reboot and the apply the upgrade. It will work in almost
all cases. I did 8 upgrades today and none failed. For some reason, I
applied the combo on two more volumes. They also did their job without
any problem.

I agree. As a rule I usually install with the combo updater, but this
time, I just couldn't be bothered.

However, a good standard practice I find works is, as you say, to check
the drive and that the system is stable *before* applying the updates.

I suggest maybe running a hardware check too. We had troubles with some
installation software with the old dual G5 until I found that one of
the high memory ram modules was in trouble. It was as if the installs
were trying to use as much ram as possible, while my apps did not
normally go there. Replaced the bad ram module and all was well after
that.
You may have a hardware problem with your machine.

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